With the end of the Patriots and the War Economy, was a definite resolution ever given? Did all the PMCs disband with the SOP system down? Did the natural Economy recover? What state was the world in? Also, did FOXALIVE shut down all the remaining Gekkos?

Clawing Werewolf: The primary antagonist faction. Formed by a merger between the PMCs Otselotovaya Khvatka and Werewolf. Aiming to take advantage of the massive debts of the War Economy and build a military and economic powerhouse. Led by the Masks, a unit made up of the best mercs in both companies: Pressure (uses Laser weaponry), Torch (uses flame weaponry), Gas (Uses biological warfare), Drone (uses remote weaponry), Claw (Melee specialist) Snuff (supposedly immortal) and their commander Blank. Intend to build a Metal Gear and seize control of indebted central american nation of San Lobos, building military state called "Dead Man's Land". Will use Metal Gear to deter foreign threat and recruit former mercs to build army and "collect" on the debts of multiple nations.

San Lobos Army: Weak and poorly trained. Many defect to Clawing Werewolf under General Domingue's command. Form a small resistance, but overall helpless against Clawing Werewolf and defectors. Could provide support to PCs.

Seal Team Four: A Navy SEAL force deployed to both remove Clawing Werewolf from power and secretly to also eliminate the marxist government of San Lobos and ensure the rise a US-friendly state. Contact was lost early into the mission. Could also support PCs and replace dead characters.

FOXHOUND: In the wake of the end of the War Economy, the US Government re-formed FOXHOUND as a Black-ops unit designed to operate in absolute secret. The PCs and their support team would be this.

Ouroboros: Secret organization formed by renegade PMC officers. Essentially the Anti-patriots. Aim to promote continuous global chaos and warfare. All commanding officers perished during the time of the War Economy, and the organization only consists of one agent, the nanomachine-enhanced super-soldier Snuff, and the AI uploaded into his machines to imitate commanding officers. Snuff believes he is part of a wide-reaching conspiracy, unaware that he is the sole force. Snuff intends to usurp control from Blank and use the Metal Gear to trigger a World War.

The PCs are FOXHOUND agents deployed to San Lobos with the goal of restablishing contact with Seal Team Four and eliminating both Clawing Werewolf and the San Lobos defecting forces, while also destroying their Metal Gear. The PCs eventually work their way to San Lobos City, where General Domingue is defeated, but the Metal Gear and much of Clawing Werewolf's forces are moved to the Dead Zone, a submarine base not unlike Arsenal Gear (but a bit smaller). Here Snuff acts, killing Blank and seizing control of the Dead Zone to attack the US with Metal Gear. The PCs would destroy the Metal Gear and "kill" Snuff (it would depend on how good they are) averting the attack and saving the world for now.

So first and foremost, does everything check out canon-wise? I'd like to think that I don't have any major clashes with continuity.

seems okay, but the best MGS rpg hack I ever saw was a story game where you played the bad guys. you rolled on table determine your combat gimmick, animal nickname and political ideology. the gm would give you plot points to compel you to rant about your ideology which you could spend to make you automatically succeed when your combat gimmick came up. There was also an option to force a retcon anytime the plot got too crazy.